title: Rectal biopsy 103

tag: subject status

tag: ajcc score

tag: overall survival (in days)


title: R3_D09_amb_penn_root_Pool2_LnRep3 (RNA-Seq)

status: Public on Nov 26 2019

type: SRA

city: Davis

first: Siobhan

last: Brady

state: CA

address: 451 Health Sciences Drive, 4303 GBSF

department: GBSF

country: USA

institute: UC Davis

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D09_amb_penn_root_Pool2_LnRep3.fq.gz

library_source: transcriptomic

data_processing:
Before and after read processing, libraries were analyzed with FastQC.
Barcodes were trimmed using fastx_trimmer (-f 9 -v -Q 33) and further quality trimmed/adapter removal was done with reaper (-geom no-bc -dust-suffix-late 10/ACTG -dust-suffix 10/ACTG --noqc -nnn-check 1/1 -qqq-check 33/10 -clean-length 30 -tri 20 -polya 5 --bcq-late)
Trimmed reads were mapped to the reference transcriptome of S. lycopersicum (v3.2) using bowtie with subsequent conversion to BAM format using samtools.
HTSeq-count was used to obtain raw counts
Differential expression was assessed with limma-voom using the voomWithQualityWeights() function.
Genome_build: ITAG3.2 (ftp://ftp.solgenomics.net/tomato_genome/annotation/ITAG3.2_release/ITAG3.2_cDNA.fasta)
Supplementary_files_format_and_content: comma separated files (one for RNA-Seq another for TRAP-Seq data) with raw counts for each sample (RNASeq tech reps are unaggregated).

molecule: total RNA

organism: Solanum pennellii

source_name: root

growth_protocol: Seeds were sterilized and sown in Profile calcined Clay media in 4-inch pots with a modified removable bottom. Plants were grown in Conviron  392 PGR15 growth chambers (Controlled Environments Ltd., Winnipeg, Manitoba, Canada).

extract_protocol:
For transcriptome profiling, root tissue from three individual plants was pooled together to yield one root sample per treatment-species combination per day on each of the three sampling days, and shoot tissue from the same three plants was pooled together to yield one shoot sample per treatment-species combination per day on each of the three sampling days.
RNAseq Library Preparation   RNAseq libraries were prepared using the method described by (Kumar et al., 2012). Briefly, for each library, the pooled root or shoot samples were homogenized in lysis and binding buffer containing beta-mercaptoethanol. Tissue was disrupted using a mortar and pestle and a Mini-beadbeater-96 high-throughput cell disruptor (BioSpec Products, Bartlesville, OK). Oligo (dT)25-coated Dynabeads (Ambion, Foster City, CA) were then added to the lysate, and mixed for 10 minutes to allow oligo (dT) beads to hybridize to poly-adenylated mRNA. cDNA was then synthesized and digested to ~300 bp fragments using NEBNext DNA fragmentase enzyme mix (NEB, Beverly, MA, USA). Library fragments greater than 300 bp were purified using Ampure XP solid phase reverse immobilization (SPRI) magnetic beads (Agencourt Bioscience, Beverly, MA, USA). For each library, one of the ninety-six unique barcoded adapters described in Kumar et al (2012) was ligated to each library, enabling multiplexing. cDNA was quantified using a SYBR-green based method on a plate reader, libraries were pooled, and fragment size and quality was checked using a BioAnalyzer (Agilent Technologies, Santa Clara, CA).  Translating Ribosome Affinity Purification (TRAP)   To determine the effects of eCO2 on the translatome of shoot tissue, transgenic S. lycopersicum and S. pennellii expressing a FLAG-epitope on the ribosomal L18 (RPL18) under the 35S promoter (Ron et al., 2013) were grown in ambient and elevated [CO2] in the same conditions and chambers as described above. At 6 and 12 DAP, tissue was collected for the Translating Ribosome Affinity Purification (TRAP) protocol. Because the biomass of plant tissues in young seedlings was small, and because the TRAP populations were segregating, we pooled multiple plants (up to 15) together to ensure that adequate mRNA for library preparation could be collected via the ribosomal pulldown.   The TRAP procedure has been described by (Zanetti et al., 2005). Briefly, tissues from transgenic plants expressing the FLAG epitope was ground in liquid nitrogen using a mortar and pestle, and homogenized in polysome extraction buffer. Samples were clarified by centrifugation and filtration through Miracloth, and clarified extract was added to magnetic beads that were coated in anti-flag antibody. Beads and extract were incubated at 4˚C using a nutator for 2 hours, and washed 6-7 times with wash buffer. Polysomes bound to magnetic beads were then frozen at -80°C until RNAseq library preparation.   RNAseq libraries were prepared from TRAP polysomes using the method described by (Townsley et al., 2015). Lysis and binding buffer containing beta-mercaptoethanol was added to anti-flag magnetic beads and bound ribosomes, allowing elution of mRNA. mRNA was then hybridized to biotin-20nt-dT oligos, allowing pulldown of mRNA out of solution with the use of magnetic streptavidin beads. mRNA was then washed with three successive buffers, eluted off of beads at 80˚C, and a secondary wash was performed, by adding more biotin-20nt-dT oligos to the mRNA, repeating the bead pulldown, and the buffer washes. mRNA was then heat-fragmented, and first and second strand cDNA was synthesized. The optimal fragment size was selected using Ampure beads, and libraries were enriched using PCR.

treatment_protocol: Chambers were set at either ambient (400 ppm) or eCO2 (700 ppm), 325 μmol m-2 s-1 PPFD, 70% Relative humidity, 16:8 light: dark schedule, and 22° C at the Controlled Environment Facility at University of California, Davis. Plants were watered every 2-3 days with 40% Long-Ashton solution containing 6 mM NH4NO3. The location of flats within each chamber and the location of plants within each flat were rotated upon every watering, and CO2 treatment assignments were rotated between chambers at every experimental replication in order to avoid any experimental artifacts caused by differences between chambers.

value: amb

tag: day

tag: r

tag: pool

tag: lnrep

tag: tissue

value: root


title: Sample 107: H11_H3

city: Stanford

first: Erin

last: Mitsunaga

address: 300 Pasteur Drive

department: Genetics

institute: Stanford University School of Medicine

data_processing:
FASTQ files were submitted to iRepertoire for analysis using their iRmap program (Wang et al., 2010).
Briefly, sequence reads were de-multiplexed according to barcode sequences at the 5’ end of reads from the BCR heavy constant regions. Reads were then trimmed according to their base qualities with a 2-base sliding window.
Trimmed paired-end reads were joined together through overlapping alignment with a modified Needleman-Wunsch algorithm.
The merged reads were mapped using a Smith-Waterman algorithm to germline V, D, J, and C reference sequences downloaded from the IMGT web site (Lefranc, 2003).
To define the CDR3 region, the position of CDR3 boundaries of reference sequences from the IMGT database were migrated onto reads through mapping results, and the resulting CDR3 regions were extracted and translated into amino acids.
Genome_build: IMGT human BCR
Supplementary_files_format_and_content: Comma-separated values files were generated by iRepertoire for each sample.  Each files contains the nucleic acid and predicted amino acid sequence of the CDR3 regions, isotypes, assigned V, D, and J genes, and read counts.

organism: Homo sapiens

source_name: B cells

extract_protocol:
Total RNA was extracted from flow cytometry-sorted human peripheral blood B cells with the Qiagen AllPrep RNA/DNA Micro Kit (Cat. # 80284) per the manufacturer's instructions.
Targeted RNA sequencing libraries were made using human B cell-specific primers from iRepertoire (Huntsville, AL) according to the company's instructions.  Briefly, two rounds of RT-PCR were performed for each chain type (heavy or light chain) and the resulting B cell receptor amplicons were sequenced.

tag: cell type

value: B cells

value: Peripheral blood

tag: subset

value: Memory

tag: chain type

value: Heavy

tag: irepertoire barcode

tag: health status

value: Healthy

tag: time point


title: Sample 106R: H11_L2R

value: Naïve

value: Light - Kappa and Lambda


title: R3_D09_amb_penn_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D09_amb_penn_root_Pool2_LnRep2.fq.gz


title: WT CT14 RNA-Seq rep2

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

data_processing:
Reads were mapped to the mouse genome build mm10 using HISAT (Kim et al. 2015), and gene expression was normalized and quantified using Cufflinks (Mortazavi et al. 2008), HTSEQ and Bedtools (Quinlan et al. 2010) by default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated using Python

organism: Mus musculus

source_name: LIVER

extract_protocol:
Mouse liver tissues were collected from XBP1Flox (n=2) and XBP1LKO (n=2) mice at 2h interval for a total of 48 hours under constant darkness condition. Total RNA was isolated from mouse liver with miRNeasy Mini Kit (Qiagen) per the manufacturer’s instructions.
Extracted RNA samples underwent quality control assessment using the RNA Pico 6000 chip on Bioanalyzer 2100 (Agilent) and were quantified with Qubit Fluorometer (Thermo Fisher). Strand-specific total mRNA-Seq libraries were prepared using the Universal Plus mRNA-Seq kit (NuGen) per the manufacturer’s instructions using 200ng of RNA. The size selection for libraries were performed using SPRIselect beads (Beckman Coulter) and purity of the libraries were analyzed using the High Sensitivity DNA chip on Bioanalyzer 2100 (Agilent).
The prepared libraries were pooled and sequenced using NoveSeq 6000 (Illumina), generating ~40 million 2×100 bp paired-end reads per samples. RNA-Seq library preparation and sequencing were performed at Univesity of Pittsburgh Medical Center (UPMC) Genome Center.

tag: gender

value: Male

tag: strain

value: C57BJ/L6 background

tag: age

value: 8-12 weeks of age

tag: genotype/variation

value: WT


title: R3_D09_amb_penn_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D09_amb_penn_root_Pool2_LnRep1.fq.gz


title: Sample 106: H11_L2


title: Rectal biopsy 61

type: RNA

city: CLEVELAND

first: Matthew

last: Kalady

state: OHIO

address: 9500 EUCLID AVE

department: Cancer Biology Department

institute: CLEVELAND CLINIC

description: Gene expression in pretreated rectal cancer biopsy measured in frozen tissue

hyb_protocol: 1.5µg of biotinylated cRNA were incubated 5 minutes at 65°C before being mixed with 20µL hybridation mix provided by the kit (Illumina, San Diego, California, USA). After being placed into the chamber, the beadchip were loaded with 30uL of cRNA per sample.  The chamber is placed 17hrs at 58°C.  Beadchips are then washed with 250mL of the E1BC solution (Illumina) before a second wash at high temperature (55°C). The beadchips are rinced with fresh E1BC buffer then submerged for 10min with 100% ethanol. The beadcips are washed for a second time at room temperature and blocked with buffer provided by the kit.

scan_protocol: Slides were scanned immediately after washing on the Beadarray Reader (illumina) with Sentrix type 6x2and Direct hyb settings. Dye chennal is set to green with green PMT sets to 100% and gain to 0.5. After measurment of the tilt and alignment of the beadchips, scann is completed and .Tiff uncompressed images are then generated

data_processing: The scanned images with .tiff format were analyzed with Beadstudio Gene expression module v3.4 using default parameters tu quantify floresence intensity and substract the background for each beadchips analyzed.

source_name: Frozen rectal cancer biopsy

label_protocol: The Biotin-labeling was done during cRNA convertion using the  TotalPrepTM RNA amplification kit (Illumina, San Diego, California, USA) . Briefly, 100ng of mRNAs were used for a two-steps reverse transcription reaction and being converted into cDNA. After elution, the cDNA are converted into cRNA using biotin-NTP mix and then purified with a filter cartbridge. After hybridization and blockage, Biotin-labeled cRNA are incubated in streptavidin-Cy3 buffer provided in the kit at room temperature for 10 min and then washed with E1BC buffer provided in the kit and dried.

extract_protocol: The mRNA were extracted from the 12 slices/biopsy using the RNAqueous Kit (Ambion, Austin, Texas, USA) according the manufacturer's protocol. Then samples were treated with  TURBO DNA‐free  (Ambion, Austin, Texas, USA) to ensure a complete degradation of genomic DNA. Concentrations of mRNAs were determined with Nanodrop (ThermoFisher, Waltham, Massachusetts, USA) and quality of the extractions was assessed by 260/280nm readings. Integrity of mRNAs was verified by migration on agarose gel 1%.

treatment_protocol: Freshly harvested, the biopsies were snap frozen at -80°C. The frozen biopsies were then embadded in medium for frozen specimen to ensure optimal cutting temperature (O.C.T). Per biopsy, 12 slices of 10µm each were cut and used for mRNA extraction.

tag: subject status

value: patient with rectal adenocarcinoma

tag: ajcc score

tag: dead (1)/alive(0)


title: R3_D09_amb_penn_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D09_amb_penn_root_Pool1_LnRep1.fq.gz

tag: day

tag: r


title: Rectal biopsy 79

tag: overall survival (in days)


title: Rectal biopsy 56


title: Rectal biopsy 84


title: WT CT14 RNA-Seq rep1


title: WT CT12 RNA-Seq rep2


title: Rectal biopsy 53


title: R3_D06_ele_penn_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D06_ele_penn_shoot_Pool2_LnRep4.fq.gz

source_name: shoot

value: ele

tag: pool

tag: lnrep

tag: tissue

value: shoot


title: Sample 105: H11_H2

tag: cell type

tag: subset

tag: chain type


title: WT CT10 RNA-Seq rep2


title: Sample 104: H11_L1

value: Immature

tag: irepertoire barcode

tag: health status

tag: time point


title: WT CT12 RNA-Seq rep1

tag: gender

tag: strain

tag: age


title: WT CT10 RNA-Seq rep1

tag: genotype/variation


title: Sample 102: H10_L4

value: Plasmacyte


title: R3_D06_ele_penn_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D06_ele_penn_shoot_Pool2_LnRep2.fq.gz


title: R3_D06_ele_penn_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D06_ele_penn_shoot_Pool2_LnRep3.fq.gz


title: Rectal biopsy 26

tag: subject status

tag: ajcc score

tag: dead (1)/alive(0)


title: Rectal biopsy 40

tag: overall survival (in days)


title: Rectal biopsy 23

value: Female


title: Rectal biopsy 30


title: Rectal biopsy 49


title: Sample 103: H11_H1

value: B cells


title: Sample 101: H10_H4

value: Peripheral blood


title: Sample 101R: H10_H4R


title: WT CT6 RNA-Seq rep2


title: WT CT6 RNA-Seq rep1


title: R3_D06_ele_penn_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D06_ele_penn_root_Pool2_LnRep4.fq.gz

tag: day

tag: r

tag: pool

value: root


title: Sample 99: H10_H3

tag: cell type

tag: tissue

value: Memory

value: Heavy


title: Sample 98: H10_L2

tag: subset

value: Naïve

tag: chain type

value: Healthy


title: R3_D06_ele_penn_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D06_ele_penn_root_Pool1_LnRep1.fq.gz

tag: lnrep


title: RBR-KO2_LD_24h_rep.2

city: Mishima

first: Takayuki

last: Fujiwara

state: Shizuoka

address: Yata 1111

country: Japan

institute: National institute of genetics

hyb_protocol: Hybridization was performed for 17 hours using Gene Expression Hybridization Kit (Agilent) according to the instruction.

scan_protocol: Hybridized microarrays were scanned using a SureScan Microarray Scanner (Agilent) and the signal intensities of oligo DNA spots were measured by Agilent Feature Extraction 12.0.3.1 (Agilent).

data_processing: The raw data set were re-scaled by a quantile-normalization method to account for the differences in individual hybridization intensities. Normalization was performed for each data set (WT1-1 to WT1-8), (CDKA-cKD1-1 to CDKA-cKD1-8), (WT2-1 to WT2-8), (CDKA-cKD2-1 to CDKA-cKD2-8), (WT3-1 to WT3-8), (RBR-KO1-1 to RBR-KO1-8), (WT4-1 to WT4-8), and (RBR-KO1-1 to RBR-KO1-8).

organism: Cyanidioschyzon merolae

source_name: C. merolae RBR-KO

label_protocol: 100 ng of total RNA was reverse transcribed using using oligo-dT primers, and then cRNAs were labeled with Cy3 while its transcription. Both reactions were performed using LowInput QuickAmp Labeling Kit One-Color (Agilent).

growth_protocol: C. merolae algal cells are cultured with aeration (3 L/min ambient air) in the 12-h light (100 μmol photon m-2 s-1) and 12-h dark cycle at 42°C.

extract_protocol: Total RNAs were isolated from frozon algal cell pellets using TRIzol(SIGMA) according to the instruction. Then, total RNAs were purified with RNeasy Kit (Qiagen).

treatment_protocol: The samples were harvested every four hours in the LD cycle, rapidly frozen in liquit nitrogen after centrifugation and then stored at −80°C until use.

value: RBR-KO

tag: sampling time

value: 30 min before the light period starts


title: RBR-KO2_LD_28h_rep.2

value: 3 h 30 min after the light period starts


title: Rectal biopsy 20

tag: gender


title: RBR-KO2_LD_20h_rep.2

value: 7 h 30 min after the dark period starts


title: Sample 105R: H11_H2R

tag: irepertoire barcode

tag: health status

tag: time point


title: Sample 97: H10_H2


title: WT CT8 RNA-Seq rep2

value: Male

tag: strain

value: C57BJ/L6 background

tag: age

value: 8-12 weeks of age

tag: genotype/variation

value: WT


title: R3_D06_ele_penn_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D06_ele_penn_shoot_Pool2_LnRep1.fq.gz

value: ele

value: shoot


title: Sample 96: H10_L1

value: B cells

value: Immature

value: Light - Kappa and Lambda


title: RBR-KO2_LD_12h_rep.2

value: 30 min before the dark period starts


title: R3_D06_amb_penn_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D06_amb_penn_shoot_Pool2_LnRep3.fq.gz

value: amb


title: WT CT8 RNA-Seq rep1


title: RBR-KO2_LD_8h_rep.2

value: 7 h 30 min after the light period starts


title: R3_D06_ele_penn_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D06_ele_penn_shoot_Pool1_LnRep1.fq.gz


title: Sample 100: H10_L3

value: Peripheral blood

value: Memory

value: Healthy


title: WT CT4 RNA-Seq rep2


title: R3_D06_amb_penn_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D06_amb_penn_shoot_Pool2_LnRep4.fq.gz


title: Sample 94: H9_L4

value: Plasmacyte

value: February 5, 2015


title: RBR-KO2_LD_4h_rep.2

value: RBR-KO

value: 3 h 30 min after the light period starts


title: R3_D06_ele_penn_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D06_ele_penn_root_Pool2_LnRep2.fq.gz

value: root


title: RBR-KO2_LD_0h_rep.2

value: 30 min before the light period starts


title: WT4_LD28h_rep.2

source_name: C. merolae 10D

value: wildtype


title: WT CT4 RNA-Seq rep1

value: Male

value: C57BJ/L6 background

value: 8-12 weeks of age

value: WT


title: R3_D06_amb_penn_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D06_amb_penn_shoot_Pool1_LnRep1.fq.gz

value: shoot


title: Sample 93R: H9_H4R

value: B cells

value: Heavy


title: RBR-KO2_LD_16h_rep.2

value: 3 h 30 min after the dark period starts


title: Rectal biopsy 16

tag: subject status

value: patient with rectal adenocarcinoma

tag: ajcc score

value: Female

tag: overall survival (in days)

tag: dead (1)/alive(0)


title: Sample 93: H9_H4

tag: cell type

value: Peripheral blood

value: Plasmacyte

value: Healthy


title: Sample 97R: H10_H2R

tag: tissue

value: Naïve


title: R3_D06_ele_penn_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D06_ele_penn_root_Pool2_LnRep1.fq.gz

value: ele

tag: day

tag: r

tag: pool

value: root


title: Sample 113: H12_H2

tag: subset

tag: chain type


title: R3_D06_ele_penn_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D06_ele_penn_root_Pool2_LnRep3.fq.gz

tag: lnrep


title: WT CT2 RNA-Seq rep2

tag: gender


title: WT CT2 RNA-Seq rep1


title: R3_D06_amb_penn_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D06_amb_penn_root_Pool2_LnRep2.fq.gz

value: amb


title: WT4_LD16h_rep.2

value: wildtype

tag: sampling time


title: WT CT0 RNA-Seq rep2

value: Male

tag: strain

value: C57BJ/L6 background


title: WT4_LD24h_rep.2

value: 30 min before the light period starts


title: Sample 95: H10_H1

value: Immature

tag: irepertoire barcode

tag: health status

tag: time point


title: WT CT0 RNA-Seq rep1

tag: age

value: 8-12 weeks of age

tag: genotype/variation

value: WT


title: R3_D06_amb_penn_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D06_amb_penn_shoot_Pool2_LnRep2.fq.gz

value: shoot


title: R3_D06_amb_penn_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D06_amb_penn_shoot_Pool2_LnRep1.fq.gz


title: XBP1s CHIP-Seq WT CT28

first: Bokai

last: Zhu

address: 100 Technology Dr, Bridgeside point

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
Duplicates were pooled at each time for subsequent ChIP-Seq analysis. The sequences identified were mapped to the mouse genome (UCSC mm10) using BOWTIE function in Galaxy. Only the sequences uniquely mapped with no more than 2 mismatches were kept and used as valid reads. PCR duplicates were also removed. Peak calling was carried out by MACS2 (version 2.1.1.20160309) in Galaxy (options --mfold 5, 50 --pvalue 1e-4), on each ChIP-seq file against the ChIP-Seq of XBP1LKO mice. To account for the different sequencing depths between samples, the signal files generated from MACS2 were RPKM normalized to sequencing depth (Meyer and Liu, 2014). Due to the robust 12h oscillation of XBP1s hepatic nuclear proteins (Cretenet et al. 2010; Zhu et al. 2017), only XBP1s cistrome exhibiting robust 12h oscillations (period between 10.5h to 13.5h; decay rate between 0.8 to 1.2; phase between 0h to 3h) are selected as bona fide XBP1s binding sites.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

extract_protocol: The DNA libraries were prepared at Univerisity of Pittsburgh and sequenced at Gene by Gene per standard protocols. DNA libraries were prepared with Ovation® Ultralow V2 DNA-Seq library preparation kit (NuGen) using 1ng input DNA. The size selection for libraries were performed using SPRIselect beads (Beckman Coulter) and purity of the libraries were analyzed using the High Sensitivity DNA chip on Bioanalyzer 2100 (Agilent). The prepared libraries pooled and sequenced using Nova-Seq 6000 SP flowcell (Illumina), generating ~30 million 75 bp single-end reads per samples.

treatment_protocol: ChIP for XBP1s was performed using anti-XBP1s antibody (Biolegend Poly6195) as previously described (Zhu et al. 2015). Briefly, mouse liver samples were submerged in PBS + 1% formaldehyde, cut into small (~1 mm3) pieces with a razor blade and incubated at room temperature for 15 minutes. Fixation was stopped by the addition of 0.125 M glycine (final concentration). The tissue pieces were then treated with a TissueTearer and finally spun down and washed twice in PBS. Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. The chromatin was enzymatically digested with MNase. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, Proteinase K and heated for reverse-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer. An aliquot of chromatin (30 μg) was precleared with protein A agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using 4 μg of antibody. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinking were reversed by incubation overnight at 65 °C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.

tag: genotype

tag: time

value: liver

tag: chip antibody

value: anti-XBP1s (biolegend 6105)


title: XBP1s CHIP-Seq XBP1 LKO

value: XBP1 LKO

tag: tissue


title: R3_D06_amb_penn_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D06_amb_penn_root_Pool2_LnRep1.fq.gz

tag: day

tag: r


title: XBP1s CHIP-Seq WT CT44


title: WT4_LD20h_rep.2

value: 7 h 30 min after the dark period starts


title: WT4_LD12h_rep.2

value: 30 min before the dark period starts


title: Sample 94R: H9_L4R

tag: cell type

value: B cells

value: Peripheral blood

tag: subset

value: Plasmacyte

value: Light - Kappa and Lambda

value: Healthy

value: February 5, 2015


title: XBP1s CHIP-Seq WT CT40

value: Male


title: R3_D06_amb_penn_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D06_amb_penn_root_Pool1_LnRep1.fq.gz

value: amb

tag: pool

tag: lnrep

value: root


title: XBP1s CHIP-Seq WT CT20

tag: gender

value: 8-12 weeks of age


title: R3_D06_amb_penn_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D06_amb_penn_root_Pool2_LnRep4.fq.gz


title: XBP1s CHIP-Seq WT CT36

tag: strain

value: WT


title: WT4_LD4h_rep.2

value: wildtype

tag: sampling time

value: 3 h 30 min after the light period starts


title: R2_D12_ele_penn_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D12_ele_penn_shoot_Pool2_LnRep4.fq.gz

value: ele

value: shoot


title: Sample 92R: H9_L3R

value: Memory

tag: chain type

tag: irepertoire barcode

tag: health status


title: XBP1s CHIP-Seq WT CT32

tag: age

value: liver

value: anti-XBP1s (biolegend 6105)


title: Sample 92: H9_L3

value: B cells

value: Peripheral blood

tag: time point


title: R3_D06_amb_penn_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D06_amb_penn_root_Pool2_LnRep3.fq.gz


title: WT4_LD8h_rep.2

tag: genotype/variation

value: 7 h 30 min after the light period starts


title: Sample 91R: H9_H3R

value: Heavy

value: Healthy


title: R2_D12_ele_penn_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D12_ele_penn_shoot_Pool2_LnRep1.fq.gz


title: Sample 91: H9_H3

value: February 5, 2015


title: XBP1s CHIP-Seq WT CT16

value: Male

tag: genotype

tag: time

tag: chip antibody


title: R2_D12_ele_penn_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D12_ele_penn_shoot_Pool2_LnRep2.fq.gz

tag: day

tag: r

tag: tissue


title: Sample 90R: H9_L2R

tag: cell type

tag: subset

value: Naïve

value: Light - Kappa and Lambda


title: XBP1s CHIP-Seq WT CT24

tag: gender

value: 8-12 weeks of age

value: WT


title: RBR-KO1_LD_24h_rep.1

value: RBR-KO

value: 30 min before the light period starts


title: WT4_LD0h_rep.2

value: wildtype


title: R2_D12_ele_penn_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D12_ele_penn_shoot_Pool2_LnRep3.fq.gz

value: ele

tag: pool

tag: lnrep

value: shoot


title: XBP1s CHIP-Seq WT CT12

tag: strain

value: liver

value: anti-XBP1s (biolegend 6105)


title: XBP1s CHIP-Seq WT CT4


title: Sample 90: H9_L2

value: B cells

value: Peripheral blood

tag: chain type

tag: irepertoire barcode


title: XBP1s CHIP-Seq WT CT8

tag: age


title: RBR-KO1_LD_28h_rep.1

tag: sampling time

value: 3 h 30 min after the light period starts


title: Sample 89R: H9_H2R

value: Heavy

tag: health status

value: Healthy

tag: time point


title: R2_D12_ele_penn_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D12_ele_penn_root_Pool2_LnRep3.fq.gz

value: root


title: RBR-KO1_LD_12h_rep.1

tag: genotype/variation

value: 30 min before the dark period starts


title: Sample 89: H9_H2

value: Naïve

value: February 5, 2015


title: Sample 88: H9_L1

value: Immature

value: Light - Kappa and Lambda


title: RBR-KO1_LD_8h_rep.1

value: RBR-KO

value: 7 h 30 min after the light period starts


title: R2_D12_ele_penn_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D12_ele_penn_root_Pool2_LnRep4.fq.gz

value: ele


title: R2_D12_ele_penn_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D12_ele_penn_shoot_Pool1_LnRep1.fq.gz

value: shoot


title: Sample 87: H9_H1


title: RBR-KO1_LD_20h_rep.1

value: 7 h 30 min after the dark period starts


title: R2_D12_ele_penn_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D12_ele_penn_root_Pool2_LnRep1.fq.gz


title: R2_D12_ele_penn_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D12_ele_penn_root_Pool1_LnRep1.fq.gz


title: WT2

city: Paris

first: Javier

last: Gilabert-Juan

address: 11, Marcelin Berthelot

department: CIRB

country: France

institute: College de France

data_processing:
RNA-Seq data analysis was performed by GenoSplice technology (www.genosplice.com). Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC (v0.10.1), Picard-Tools (v1.119), Samtools (v0.1.19) and rseqc (v2.4). Reads were mapped using STAR (v2.3.0) (Dobin et al., 2013).
Gene expression was estimated using Mouse FAST DB v2013_1 annotations. Genes were considered as expressed if their rpkm value was greater than 97.5% of the background rpkm value based on intergenic regions. Raw count data normalization and differential expression analysis were then performed using Deseq (v1.12.1). Results were considered statistically significant for unadjusted p-values ≤ 0.05 and fold-changes ≥ 1.5.
The mouse dataset was annotated with human Ensembl gene ID using BiomaRt Bioconductor R package (Naro et al., 2017; Noli et al., 2015) and selecting human genes that were ‘one-to-one’ orthologues with mouse genes. As previously described (Delahaye-Duriez et al., 2016), we generated a gene-level score reflecting the significance and the intensity of differential expression (multiplying the –log10 of p value by the log-transformed fold change). This score was used as a metric to ‘rank’ genes to test using Gene set enrichment analysis (GSEA) if gene sets defined in the Molecular Signatures database (MSigDB v5.2) occupy higher (or lower) positions in the ranked gene list than what it would be expected by chance (Subramanian et al., 2005). The enrichment was tested for several sets of genes of the MSigDB: Gene ontology (GO) biological process, cellular component and molecular functions, Reactome pathways, and Hallmark gene sets. The MSigDB hallmark gene sets is a collection of 50 gene sets that provide coherently expressed signatures derived by aggregating many MSigDB gene sets (Molecular Signatures Database v5.2) to represent well-defined biological states or processes (Liberzon et al., 2015). Gene set enrichment scores (NES, p value, FDR and FWER) were provided in the GSEA output format developed by Broad Institute of MIT and Harvard (permutations = 10,000).
Supplementary_files_format_and_content: normalized counts

source_name: Neural progenitor cells

growth_protocol: Mouse dorsal telencephalon was dissected from E12.5 brains in DMEM/F12 medium (Invitrogen). Cell suspension was obtained by mechanical dissociation. NPCs from each telencephalon were grown individually as neurospheres in 6 well plates and in DMEM/F12 medium supplemented with 1xN2 and 0.5xB27, 10 ng/ml FGF (Invitrogen), 10 μg/ml Insulin and 10 ng/ml bFGF (Sigma Aldrich). Two days after the culture start, wild type (WTNPCs) or Mcph1 KO (KONPCs) primary cultures were pooled by two or three in a T75 flask for further expansion during two to three days. At this stage, neurospheres were pelleted for protein extraction or RNA extraction, or mechanically dissociated for seeding on gelatin-coated dishes, glass coverslips in 24-well plates or IBIDI slides (IBIDI). Attached cells were cultured in DMEM medium (Invitrogen) containing 10% fetal bovine serum, and containing either i) 4,5 g/L Glucose, 1mM sodium pyruvate and 1mM Glutamine (GPGln complete medium); ii) 2mM sodium pyruvate and 1mM Glutamine (PGln medium); iii) 1mM Glutamine only (Gln medium). Cells were then maintained in culture for four days.

extract_protocol:
Total RNA was extracted from WTNPCs and WTNPCs. Sample quality and quantification were assessed on Experion chips (Bio-Rad). Twin samples were pooled according to genotype and matching amounts.
Library preparation and Illumina sequencing were performed on wild type and Mcph1 KO samples, two of each, at the Genomic Platform of the Ecole Normale Superieure (Paris, France). Ribosomal RNA depletion was performed with the Ribo-Zero kit (Epicentre), using 1.5 μg of total RNA. Libraries were prepared using the strand specific RNA-Seq library preparation ScriptSeq V2 kit (Epicentre). Libraries were multiplexed by 4 on 1 flow cell lane. A 75bp read sequencing was performed on a HiSeq 1500 device (Illumina). A mean of 39.3 ± 7 million passing Illumina quality filter reads was obtained for each of the 4 samples.

value: Neuroephitelial cells

tag: genotype

value: WT


title: Mcph1 KO1

value: Mcph1 KO


title: Mcph1 KO2


title: R2_D12_ele_penn_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D12_ele_penn_root_Pool2_LnRep2.fq.gz

tag: day


title: Sample 87R: H9_H1R

value: B cells

value: Peripheral blood


title: Sample 85: H8_H4

value: Plasmacyte

value: Heavy

value: Healthy

value: February 2, 2015


title: XBP1s CHIP-Seq WT CT0

value: Male

value: 8-12 weeks of age

tag: time

value: liver

tag: chip antibody

value: anti-XBP1s (biolegend 6105)


title: Sample 88R: H9_L1R

tag: cell type

tag: tissue

value: Immature

value: Light - Kappa and Lambda

value: February 5, 2015


title: RBR-KO1_LD_16h_rep.1

value: RBR-KO

value: 3 h 30 min after the dark period starts


title: RBR-KO1_LD_4h_rep.1

value: 3 h 30 min after the light period starts


title: Sample 83: H8_H3

tag: subset

value: Memory


title: RBR-KO1_LD_0h_rep.1

value: 30 min before the light period starts


title: WT3_LD28h_rep.1

value: wildtype


title: Sample 86: H8_L4

value: B cells

value: Peripheral blood

value: Plasmacyte


title: WT1

value: Neuroephitelial cells

value: WT


title: Sample 84: H8_L3

value: Healthy

value: February 2, 2015


title: R2_D12_amb_penn_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D12_amb_penn_shoot_Pool2_LnRep3.fq.gz

value: amb

tag: r

tag: pool

value: shoot


title: R2_D12_amb_penn_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D12_amb_penn_shoot_Pool2_LnRep1.fq.gz

tag: lnrep


title: R2_D12_amb_penn_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D12_amb_penn_shoot_Pool2_LnRep2.fq.gz


title: R2_D12_amb_penn_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D12_amb_penn_shoot_Pool2_LnRep4.fq.gz


title: Sample 82: H8_L2

value: Naïve

tag: chain type

value: Light - Kappa and Lambda


title: R2_D12_amb_penn_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D12_amb_penn_shoot_Pool1_LnRep1.fq.gz


title: R2_D12_amb_penn_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D12_amb_penn_root_Pool2_LnRep3.fq.gz

value: root


title: Sample 78: H7_L4

tag: irepertoire barcode

value: January 26, 2015


title: WT3_LD16h_rep.1

value: 3 h 30 min after the dark period starts


title: R2_D12_amb_penn_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D12_amb_penn_root_Pool2_LnRep2.fq.gz


title: WT3_LD20h_rep.1

value: 7 h 30 min after the dark period starts


title: WT3_LD24h_rep.1

value: 30 min before the light period starts


title: Sample 81: H8_H2

value: Heavy


title: Sample 80: H8_L1

value: B cells

value: Immature


title: G1-arrested HA-CDKA-cKD2_28h_rep.2

source_name: C. merolae CDKA-cKD

value: HA-CDKA-conditional knockdown

value: 3 h 30 min after the light period starts


title: PRMT6_shRNA2_replicate2

city: san francisco

first: Yen-Sin

last: Ang

state: CALIFORNIA

address: 1650 Owens Street

institute: Gladstone Institute, UCSF

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was VST transformed, RSN normalized in R using LUMI package

label: biotin

source_name: Embryonic Stem Cell

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: CCE (Stem Cell Tech) ES cells, maintained feeder-free, were used for transient shRNA knockdown in DMEM media supplemented with 15% FBS, 100 mM MEM non-essential amino acids, 0.1 mM 2-mercaptoethanol, 1 mM l-glutamine and 1000 / ml of LIF (Chemicon).

extract_protocol: total RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

treatment_protocol: shRNA (Prmt6 or GFP) cloned into pSuper.puro (Oligoengine) were transfected into CCE using Lipofectamine. 18h later, puromycin (1.5ug/ml) containing media was changed and selected for 4days.

tag: cell line

value: CCE

tag: shRNA


title: PRMT6_shRNA1_replicate1


title: R2_D12_amb_penn_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D12_amb_penn_root_Pool2_LnRep4.fq.gz


title: GFP_shRNA_replicate1

value: GFP


title: Sample 79: H8_H1

value: Peripheral blood

tag: health status

value: Healthy

value: February 2, 2015


title: PRMT6_shRNA1_replicate2


title: Sample 76: H7_L3

value: Memory

tag: time point


title: WT3_LD4h_rep.1

tag: genotype/variation

value: wildtype

tag: sampling time


title: 24_hpi_R3

city: Tottori

first: Mostafa

last: Abdelrahman

address: Hamasaka

department: Arid Land Research Center

institute: Tottori University

data_processing:
Illumina Casava1.7 software used for basecalling.
FastQC software used to make quality check.
Cutadapt used to remove sequence adaptors and low quality reads.
Tophat2 used for mapping reads.
Bedtools used for quantification of gene expression.
Genome_build: Asparagus officinalis reference genome Asopf V.1
Supplementary_files_format_and_content: *.gtf: GTF files include read counts.

organism: Asparagus kiusianus

extract_protocol:
Total RNA was harvested using RNA extraction kit (Qiagen) from stem samples. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: genotype

value: Resistant

value: Stem

tag: infection

value: Phomopsis asparagi

value: 24 hpi


title: 48_hpi_R3

value: 48 hpi


title: Sample 77: H7_H4

value: Plasmacyte

value: Heavy

value: January 26, 2015


title: 48_hpi_R1


title: R2_D12_amb_penn_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D12_amb_penn_root_Pool2_LnRep1.fq.gz

value: amb

tag: day

value: root


title: WT3_LD8h_rep.1

value: 7 h 30 min after the light period starts


title: GFP_shRNA_replicate2

value: CCE

value: GFP


title: Sample 75: H7_H3

tag: cell type

value: B cells

value: Peripheral blood

value: Healthy


title: WT3_LD12h_rep.1

value: wildtype

value: 30 min before the dark period starts


title: PRMT6_shRNA2_replicate1


title: 48_hpi_R2

value: Resistant

tag: tissue

value: Stem


title: R2_D12_amb_penn_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D12_amb_penn_root_Pool1_LnRep1.fq.gz


title: Sample 74: H7_L2

tag: subset

value: Naïve

value: Light - Kappa and Lambda


title: Sample 73: H7_H2


title: Sample 72: H7_L1

value: Immature


title: 24_hpi_R2

value: Phomopsis asparagi

value: 24 hpi


title: G1-arrested HA-CDKA-cKD2_24h_rep.2

value: HA-CDKA-conditional knockdown

value: 30 min before the light period starts


title: G1-arrested HA-CDKA-cKD2_20h_rep.2

value: 7 h 30 min after the dark period starts


title: R2_D09_ele_penn_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D09_ele_penn_shoot_Pool2_LnRep4.fq.gz

value: ele

tag: r

value: shoot


title: R2_D09_ele_penn_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D09_ele_penn_shoot_Pool2_LnRep2.fq.gz

tag: pool


title: R2_D09_ele_penn_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D09_ele_penn_shoot_Pool2_LnRep3.fq.gz

tag: lnrep


title: Control_R3

description: Control

value: Control


title: G1-arrested HA-CDKA-cKD2_12h_rep.2


title: Control_R1

description: Control


title: 24_hpi_R1


title: G1-arrested HA-CDKA-cKD2_16h_rep.2

value: 3 h 30 min after the dark period starts


title: R2_D09_ele_penn_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D09_ele_penn_root_Pool2_LnRep4.fq.gz

value: root


title: phyCnull_rep3

city: Harpenden

first: Stephen

last: Pearce

state: Hertfordshire

address: West Common

department: Sustainable Soils and Crops

country: United Kingdom

institute: Rothamsted Research

description: Triticum turgidum L. subsp. durum (Desf.)

data_processing:
Bases were called at the UC Davis Genome Center using CASAVA1.5
Raw reads were trimmed for adapter contamination using "Scythe" (Default options, https://github.com/vsbuffalo) and for quality using “Sickle” (Default options except –l 25 –q 25, https://github.com/najoshi/sickle).
Trimmed reads were mapped to A and B homoeolgous chromosomes from the IWGSC RefSeqv1.0 wheat genome assembly from the hexaploid wheat variety ‘Chinese Spring’. Reads were aligned using GSNAP(l) (version 03-06-2016, default parameters except -m 4 -n 1 -N 1 -A sam).
Uniquely mapped reads were counted with ht-seq count (-m union) (http://www-huber.embl.de/users/anders/HTSeq/doc/index.html) using high confidence and low confidence gene models extracted from IWGSC RefSeqv1.0 annotations.
Gene loci with no raw count values greater than or equal to three in any replicate of any of the three genotypes were excluded from subsequent analyses.
Genome_build: IWGSC RefSeqv1.0
ftp://ftp.ensemblgenomes.org/pub/plants/release-45/fasta/triticum_aestivum/dna/
GFF3 files for annotations of all genes can be downloaded at the following link: https://urgi.versailles.inra.fr/download/iwgsc/IWGSC_RefSeq_Annotations/v1.0/
Supplementary_files_format_and_content: Tabular raw count and processed Transcripts Per Million (TPM) for each gene locus.

organism: Triticum turgidum subsp. durum

source_name: Fully-extended third leaf

growth_protocol: Plants were grown in a Conviron PGR15 growth chamber at UC Davis, CA, in 8hr light/16hr dark conditions with a light intensity of 260µM m-2 s-1 and 20 °C day/ 18 °C night temperatures.

extract_protocol:
Total RNA was extracted from the youngest fully-expanded leaf of eight-week-old plants using the Spectrum™ Plant Total RNA Kit (Sigma-Aldrich, St. Louis, MO).
RNA-seq libraries were constructed using the TruSeq™ RNA library prep kit v2 (Illumina, San Diego, CA) according to the manufacturer's instructions and their quality determined by running samples on a high-sensitivity DNA chip on a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: Fully-extended third leaf

value: phyCnull


title: G1-arrested HA-CDKA-cKD2_0h_rep.2


title: G1-arrested HA-CDKA-cKD2_8h_rep.2

value: 7 h 30 min after the light period starts


title: Control_R2

description: Control

value: Resistant

value: Stem


title: Sample 71: H7_H1

value: B cells

value: Peripheral blood

tag: chain type

value: Heavy

value: Healthy

value: January 26, 2015


title: R2_D09_ele_penn_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D09_ele_penn_root_Pool2_LnRep3.fq.gz


title: G1-arrested HA-CDKA-cKD2_4h_rep.2

value: HA-CDKA-conditional knockdown

value: 3 h 30 min after the light period starts


title: WT2_LD24h_rep.2

value: wildtype

value: 30 min before the light period starts


title: Sample 70: H6_L4

value: Plasmacyte

value: Light - Kappa and Lambda

tag: irepertoire barcode

value: January 19, 2015


title: R2_D09_ele_penn_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D09_ele_penn_shoot_Pool1_LnRep1.fq.gz

value: ele

value: shoot


title: phyCnull_rep4

value: Fully-extended third leaf

value: phyCnull


title: Sample 69: H6_H4


title: phyCnull_rep1


title: R2_D09_ele_penn_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D09_ele_penn_root_Pool2_LnRep1.fq.gz

value: root


title: phyCnull_rep2


title: WT2_LD28h_rep.2


title: Sample 66: H6_L2

value: B cells

value: Naïve


title: R2_D09_ele_penn_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D09_ele_penn_root_Pool2_LnRep2.fq.gz


title: phyBnull_rep3

value: phyBnull


title: Sample 68: H6_L3

value: Peripheral blood

value: Memory

value: Healthy


title: Sample 67: H6_H3

value: Heavy


title: R2_D09_ele_penn_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D09_ele_penn_shoot_Pool2_LnRep1.fq.gz


title: R2_D09_amb_penn_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D09_amb_penn_shoot_Pool2_LnRep4.fq.gz

value: amb


title: WT2_LD20h_rep.2

value: wildtype

value: 7 h 30 min after the dark period starts


title: phyBnull_rep4


title: Sample 65: H6_H2


title: R2_D09_ele_penn_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D09_ele_penn_root_Pool1_LnRep1.fq.gz


title: WT2_LD16h_rep.2

value: 3 h 30 min after the dark period starts


title: WT_rep4

value: WT


title: R2_D09_amb_penn_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D09_amb_penn_shoot_Pool2_LnRep1.fq.gz


title: WT2_LD0h_rep.2

value: 30 min before the light period starts


title: Sample 61: I1_4_H4

value: Plasmacyte

value: First Infection

value: December 16, 2014


title: Sample 60: I1_4_L3

value: Light - Kappa and Lambda


title: WT2_LD12h_rep.2

value: 30 min before the dark period starts


title: phyBnull_rep2

value: Fully-extended third leaf


title: WT2_LD8h_rep.2

value: 7 h 30 min after the light period starts


title: G1-arrested HA-CDKA-cKD1_24h_rep.1

value: HA-CDKA-conditional knockdown


title: Sample 64: H6_L1

value: B cells

value: Peripheral blood

value: Immature

value: January 19, 2015


title: R2_D09_amb_penn_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D09_amb_penn_root_Pool2_LnRep4.fq.gz

value: amb

value: root


title: Sample 63: H6_H1

value: Heavy

value: Healthy


title: R2_D09_amb_penn_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D09_amb_penn_shoot_Pool2_LnRep3.fq.gz

value: shoot


title: Sample 62: I1_4_L4

value: Plasmacyte


title: R2_D09_amb_penn_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D09_amb_penn_shoot_Pool2_LnRep2.fq.gz


title: phyBnull_rep1

value: phyBnull


title: WT2_LD4h_rep.2

value: wildtype

value: 3 h 30 min after the light period starts


title: G1-arrested HA-CDKA-cKD1_20h_rep.1

value: 7 h 30 min after the dark period starts


title: WT_rep3

value: Fully-extended third leaf

value: WT


title: Sample 58: I1_4_L2

value: Naïve

value: Light - Kappa and Lambda

value: First Infection

value: December 16, 2014


title: G1-arrested HA-CDKA-cKD1_16h_rep.1

value: HA-CDKA-conditional knockdown

value: 3 h 30 min after the dark period starts


title: Sample 57: I1_4_H2

value: B cells

value: Peripheral blood


title: R2_D09_amb_penn_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D09_amb_penn_root_Pool2_LnRep2.fq.gz

value: amb

value: root


title: WT3_LD0h_rep.1

value: 30 min before the light period starts


title: WT_rep2


title: Sample 56: I1_4_L1

value: Immature


title: Sample 59: I1_4_H3

value: Memory

value: Heavy


title: R2_D09_amb_penn_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D09_amb_penn_root_Pool2_LnRep1.fq.gz


title: R2_D09_amb_penn_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D09_amb_penn_root_Pool2_LnRep3.fq.gz


title: G1-arrested HA-CDKA-cKD1_28h_rep.1

value: 3 h 30 min after the light period starts


title: WT_rep1

value: Fully-extended third leaf


title: R2_D09_amb_penn_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D09_amb_penn_shoot_Pool1_LnRep1.fq.gz

value: shoot


title: R2_D09_amb_penn_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D09_amb_penn_root_Pool1_LnRep1.fq.gz


title: T2P-3

city: Nanjing

first: Chen

last: Jishuang

state: Jiangsu

address: NO.30 Puzhu Road(S)

department: College of Biotechnology and Pharmaceutical Engineering

country: China

institute: Nanjing Tech University

description: Pinellia ternata (Thunb.) Breit

data_processing:
We removed adaptor sequences, poly-N reads and low quality reads using FastQC (V 0.11.5) and Trimmomatic (V 0.36) software to obtain clean reads from raw data (containing more than 50% bases with Q ≤ 30)
We used Trinity software to perform de novo assembly with a k-mer length of 25 and other default parameters. The transcripts were clustered with a TGI clustering tool, and the longest transcripts were defined as unigenes.
We used BLASTX program with E-value of 10-5  to search functional annotation in the multiple protein databases, such as Swiss-Prot databases, Protein family (Pfam) databases, EggNOG databases, KEGG databases and GO databases
RSEM was used to calculate FPKM in each sample. Then, the DESeq R software package was used for comparing differential expression analysis between T2 line and T2Plus line. In multiple tests and analysis, we used FDR to identify the P-value threshold
Supplementary_files_format_and_content: FPKM

organism: Pinellia ternata

source_name: seedling

growth_protocol: At 30 days after planting, seedlings are collected

extract_protocol:
Five seedlings collected from each group were mixed and thoroughly ground to powder  with liquid nitrogen, and approximately 50 mg per pooled sample was prepared to use. Total RNA was isolated from each replicated sample according to the instructions of OmniPlant RNA Kit  (CWBIO, Beijing, China)
We constructed the cDNA library using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA); brief steps are described below. Firstly, the mRNA was enriched by oligo (dT)-attached magnetic beads and fragmented into short pieces, which were taken as templates for the first-strand and second-strand cDNA synthesis.  Then, the remaining overhangs into blunt ends were converted by ligase and polymerase. The resulting fragments were end-repaired by inserting an “A” base to the 3’ ends of the cDNA. And the NEBNext adapters with a hairpin loop structure were ligated to fragments. To select suitable cDNA fragments, Agencourt AMPure XP 60ml Kit (Beckman Coulter, USA) was applied to purify the library fragments. Next, the products amplified by polymerase chain reaction (PCR), which were used to create sequencing libraries.  And 350-450 bp fragments were recovered using QIAquick Gel Extraction Kit (QIAGEN, Germany). It’s crucial of quality testing for the library to ensure that the library meets the requirements of sequencing

tag: age

value: 30 days after planting

tag: ploidy

value: sixteen ploid (2n=16*13=208)

value: seedling


title: R2_D06_ele_penn_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D06_ele_penn_shoot_Pool2_LnRep4.fq.gz

value: ele


title: R2_D06_ele_penn_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D06_ele_penn_shoot_Pool2_LnRep3.fq.gz


title: T2P-1

description: Pinellia ternata (Thunb.) Breit


title: G1-arrested HA-CDKA-cKD1_12h_rep.1

value: HA-CDKA-conditional knockdown

value: 30 min before the dark period starts


title: T2P-2

description: Pinellia ternata (Thunb.) Breit


title: T2-2

description: Pinellia ternata (Thunb.) Breit


title: Sample 54: I1_3_L4

value: B cells

value: Plasmacyte

value: Light - Kappa and Lambda

tag: health status

value: First Infection

value: December 13, 2014


title: R2_D06_ele_penn_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D06_ele_penn_shoot_Pool2_LnRep2.fq.gz


title: Sample 53: I1_3_H4

value: Peripheral blood

tag: time point


title: Sample 55: I1_4_H1

value: Immature

value: December 16, 2014


title: Sample 52: I1_3_L3

value: Memory


title: T2-1

description: Pinellia ternata (Thunb.) Breit


title: G1-arrested HA-CDKA-cKD1_8h_rep.1

tag: genotype/variation

value: 7 h 30 min after the light period starts


title: G1-arrested HA-CDKA-cKD1_0h_rep.1

tag: sampling time

value: 30 min before the light period starts


title: WT1_LD28h_rep.1

value: wildtype

value: 3 h 30 min after the light period starts


title: G1-arrested HA-CDKA-cKD1_4h_rep.1


title: R2_D06_ele_penn_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D06_ele_penn_shoot_Pool2_LnRep1.fq.gz

value: shoot


title: Sample 51: I1_3_H3

value: Heavy


title: R2_D06_ele_penn_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D06_ele_penn_shoot_Pool1_LnRep1.fq.gz

value: ele


title: WT1_LD24h_rep.1


title: WT1_LD20h_rep.1

value: 7 h 30 min after the dark period starts


title: R2_D06_ele_penn_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D06_ele_penn_root_Pool2_LnRep3.fq.gz

value: root


title: WT1_LD16h_rep.1

value: 3 h 30 min after the dark period starts


title: R2_D06_ele_penn_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D06_ele_penn_root_Pool2_LnRep4.fq.gz


title: Sample 49R: I1_3_H2R

value: B cells

value: Naïve


title: T2-3

description: Pinellia ternata (Thunb.) Breit

value: 30 days after planting

value: seedling


title: Sample 48: I1_3_L1

value: Peripheral blood

value: Immature

value: Light - Kappa and Lambda

value: First Infection

value: December 13, 2014


title: Sample 47: I1_3_H1


title: WT1_LD8h_rep.1

value: wildtype

value: 7 h 30 min after the light period starts


title: WT1_LD4h_rep.1

value: 3 h 30 min after the light period starts


title: Experimental cDNA replicate 3 ("13") for MPRA1

city: New Haven

first: James

middle: Patrick

last: Noonan

state: CT

address: 333 Cedar Street

institute: Yale University

description:
MPRA1_cDNA_rep3
Experimental cDNA library barcode tag sequencing
COUNTS_ANNOTATED.txt.gz

data_processing:
Basecalling performed with CASSAVA
Inert library reads were trimmed using fastx_trimmer (options -Q 33 -f 10) and read pais were aligned using PEAR (option -q 33). Adapter sequences were trimmed using Cutadapt, first the adapters on either side of the construct and finally the construct consisting of enhancer fragment-adapter-barcode tag was split at the adapter into fragment and adapter (option -e 0.16). Fragment sequences were aligned to the fragment library using Bowtie2.
Competent library and experimental MPRA reads containing barcode tags were trimmed using fastx_trimmer (options -Q 33 -l 133 (read 1) -l 126 (read 2) and read pairs were aligned using PEAR (option -q 33). Adapter sequences were trimmed using Cutadapt (option -e 0.16).
ATAC-seq reads were mapped using Bowtie2 (option -X 2000). Reads mapping to the mitochondrion or to ENCODE-defined black listed regions were removed. Peaks were called with MACS2 (options -B --nomodel --shift -25 --extsize 50).
Genome_build: GRCh37/hg19 (ATAC-seq)
Supplementary_files_format_and_content: MPRA count files contain raw counts of MPRA reads mapped to their barcode tag and fragment of origin plus annotations.

organism:
Pan troglodytes
Homo sapiens

source_name: synthetic

growth_protocol: Neural stem cells were grown in DMEM/F12 with GlutaMAX, StemPro Neural Supplement, bFGF, EGF added in flasks coated with Matrigel at 37°C and 5% CO2. Cells were passaged using Accutase every 48 hours.

extract_protocol:
Inert and competent libraries were sequenced from plasmid PCR amplicons. Experimental libraries were extracted from NSCs using Qiagen Allprep and MinElute PCR Purification kits (pDNA, 5% of each sample) and Qiagen RNeasy Mini kit (cDNA, 95%). cDNA was synthesized using Invitrogen SuperScript III reverse transcription kit and using a mixture between a custom, library-specific primer and oligo-dT primers (MPRA1) or only custom primer (MPRA2).
We amplfied the library amplicon using qRT-PCR to stop amplification in the exponential phase. pDNA and cDNA libraries were then paired-end sequenced for 150 cycles on an Illumina HiSeq 4000s (MPRA1) or NovaSeq 6000s (MPRA2), including 5% phi-X spike-in.

treatment_protocol: MPRA libraries were transfected using a Lonza Nucleofector 2b and grown for 6 hours post transfection.

value: H9-derived Neural Stem Cells

tag: passage


title: R2_D06_ele_penn_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D06_ele_penn_root_Pool2_LnRep2.fq.gz

value: ele


title: R2_D06_ele_penn_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D06_ele_penn_root_Pool1_LnRep1.fq.gz


title: Sample 50: I1_3_L2


title: Experimental cDNA replicate 4 ("23") for MPRA1

description:
MPRA1_cDNA_rep4
Experimental cDNA library barcode tag sequencing
COUNTS_ANNOTATED.txt.gz


title: Experimental cDNA replicate 2 ("22") for MPRA1

description:
MPRA1_cDNA_rep2
Experimental cDNA library barcode tag sequencing
COUNTS_ANNOTATED.txt.gz


title: Experimental cDNA replicate 1 ("12") for MPRA1

description:
MPRA1_cDNA_rep1
Experimental cDNA library barcode tag sequencing
COUNTS_ANNOTATED.txt.gz


title: Experimental plasmid DNA replicate 4 ("23") for MPRA1

description:
MPRA1_pDNA_rep4
Experimental plasmid DNA library barcode tag sequencing
COUNTS_ANNOTATED.txt.gz


title: Sample 49: I1_3_H2

value: Heavy


title: R2_D06_amb_penn_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D06_amb_penn_shoot_Pool2_LnRep4.fq.gz

value: amb

value: shoot


title: WT1_LD0h_rep.1

value: 30 min before the light period starts


title: R2_D06_amb_penn_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D06_amb_penn_shoot_Pool2_LnRep3.fq.gz


title: Sample 46: I1_2_L4

value: B cells

value: Plasmacyte

value: December 9, 2014


title: R2_D06_ele_penn_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D06_ele_penn_root_Pool2_LnRep1.fq.gz

value: root


title: R2_D06_amb_penn_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D06_amb_penn_shoot_Pool2_LnRep2.fq.gz


title: Sample 45: I1_2_H4

value: Peripheral blood


title: Sample 43: I1_2_H3

value: Memory


title: Sample 44: I1_2_L3

value: Light - Kappa and Lambda

value: First Infection


title: R2_D06_amb_penn_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D06_amb_penn_shoot_Pool2_LnRep1.fq.gz


title: WT1_LD12h_rep.1

value: wildtype

value: 30 min before the dark period starts


title: Sample 42: I1_2_L2

value: Naïve


title: Sample 41: I1_2_H2


title: Experimental plasmid DNA replicate 3 ("13") for MPRA1

description:
MPRA1_pDNA_rep3
Experimental plasmid DNA library barcode tag sequencing
COUNTS_ANNOTATED.txt.gz

value: H9-derived Neural Stem Cells


title: R2_D06_amb_penn_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D06_amb_penn_root_Pool2_LnRep4.fq.gz


title: R2_D06_amb_penn_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D06_amb_penn_shoot_Pool1_LnRep1.fq.gz


title: Experimental plasmid DNA replicate 2 ("22") for MPRA1

description:
MPRA1_pDNA_rep2
Experimental plasmid DNA library barcode tag sequencing
COUNTS_ANNOTATED.txt.gz


title: Experimental plasmid DNA replicate 1 ("12") for MPRA1

description:
MPRA1_pDNA_rep1
Experimental plasmid DNA library barcode tag sequencing
COUNTS_ANNOTATED.txt.gz


title: Competent library for MPRA1

description:
MPRA1_competent
Competent library was sequenced as a complexity control prior to transfection
COUNTS_ANNOTATED.txt.gz


title: Sample 39: I1_2_H1

value: Immature


title: Sample 38: I1_1_L4

value: December 7, 2014


title: R2_D06_amb_penn_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D06_amb_penn_root_Pool2_LnRep3.fq.gz

value: amb


title: Sample 40: I1_2_L1


title: R2_D06_amb_penn_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D06_amb_penn_root_Pool2_LnRep1.fq.gz


title: R2_D06_amb_penn_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D06_amb_penn_root_Pool2_LnRep2.fq.gz


title: R2_D06_amb_penn_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D06_amb_penn_root_Pool1_LnRep1.fq.gz


title: Sample 36: I1_1_L3


title: Sporadic MPNST - resection [sMPNST11]

city: Rotterdam

first: Erik

last: Wiemer

address: Wytemaweg 80

department: Medical Oncology

country: Netherlands

institute: Erasmus University Medical Center

description:
sMPNST11
Primary tumor

data_processing: The expression (CT value) of a specific miRNA in a sample was normalized to the median CT of all detectable miRNAs in that sample. Subsequently the normalized relative expression (2-ΔCT) was calculated for each miRNA. The normalized miRNA expression data were log 2 transformed and median centered to acquire the relative expression values that were used for hierarchical clustering analyses using Cluster-3.0 and Java TreeView for visualization. The clustering was based on the uncentered correlation as a distance metric using average linkage. A Student T-test was used to determine statistical significance between distinct groups of expression data and the Benjamini-Hochberg false discovery rate (FDR) was used to control for multiple testing.

label: FAM

source_name: formalin-fixed paraffin embedded tumor material

label_protocol: The miRNA expression profiles were determined in FFPE samples using TaqMan™ Low Density Array (TLDA) Human MicroRNA Cards (A card v2.0, B card v3.0; Applied Biosystems/Thermo Fisher Scientific). First, two pools of cDNA were prepared using Megaplex™ RT Primers Human Pools (pool A v2.1, pool B v3.0) and a TaqMan™ microRNA Reverse Transcription kit (Applied Biosystems/Thermo Fisher Scientific). Second, a pre-amplification step was conducted using Megaplex™ PreAmp Primers Human Pools (pool A v2.1, pool B v3.0; Applied Biosystems/Thermo Fisher Scientific) together with the TaqMan™ PreAmp Master Mix (Applied Biosystems/Thermo Fisher Scientific). The resulted products were mixed with TaqMan™ Universal PCR Master Mix No AmpErase™ UNG and individually added to human microRNA A or B cards. The TLDA cards were analyzed using a 7900HT Fast Real-Time PCR system (Applied Biosystems).

extract_protocol: Total RNA was extracted from 5-6 20 µm sections from each FFPE tumor sample using the RecoverAll total nucleic acid isolation kit (Ambion / Life Technologies) according to the manufacturer’s recommendations.

treatment_protocol: Patients diagnosed with sporadic MPNST were identified in the Erasmus Medical Center files. From the Erasmus MC tissue bank archival formalin-fixed paraffin-embedded (FFPE) tissue blocks from resection material of the untreated, primary tumors were collected. Hematoxylin-eosin-stained sections of these samples were examined by an expert pathologist to confirm the initial histopathological diagnosis.

tag: diagnosis

value: Sporadic MPNST

value: Sporadic malignant peripheral nerve sheath tumor


title: Plasma, healthy [Con-17 Vumc]

city: Amsterdam

first: Elisa

last: Giovannetti

address: De Boelelaan 1117

institute: VUmc

description: Con-17 Vumc

data_processing: All RT-PCR experiments and analysis were performed by Exiqon, Denmark. The amplification curves were analyzed using the Roche LC software, both for determination of Cq and for melting curve analysis. The amplification efficiency was calculated using algorithms similar to the LinReg software. Using NormFinder Software, the best normalizer was found to be the average of assays detect in all samples. All data was normalized to the average of assays detected in all samples: average detected in all samples - assay Cq value. The 'Matrix non-normalized' file contains the raw data for all samples as Cq values. MicroRNAs not detected are indicated by ND in the raw data sheet. The 'Matrix normalized' file contains the normalized data. A higher value thus indicates that the microRNA is more abundant in the particular sample. The 'Fold change' template contains the comparisons made between the groups. Three comparisons were made: before treatment expression of non-progressive compared to progressive patients (displayed in Fold change 1), after compared to before treatment of non-progressive patients (displayed in Fold change 2), and of progressive patients (displayed in Fold change 3). The Fold change was calculated by the equation of -2^-ddCt for down-regulated microRNAs and 2^ddCq for up-regulated microRNAs. A paired t-test was used to compare before and after treatment expression, unpaired t-test for non-progressive versus progressive.

label: SYBR Green

source_name: Plasma

label_protocol: All experiments were conducted at Exiqon Services, Denmark. RNA was reverse transcribed using the miRCURY LNA Universal cDNA synthesis kit (Exiqon). cDNA was diluted ans assayed in PCR reactions according to the protocol for miRCURY LNA Universal RT microRNA PCR (Exiqon). MicroRNA expression was assessed on themicroRNA PCR Human panel i+II using Exiqon SYBR Green Master Mix, including Negative controls. Amplification was performed in a Roche Lightcycler 480 Real-Time PCR system in a 384 wells plate.

extract_protocol: Total RNA was extracted from plasma using Exiqon's miRCURY Small RNA isolation Kit for Biofluids.

tag: sex (m/f)

value: M

tag: histopathological diagnosis

value: Healthy


title: Sample 32: I1_1_L1

tag: cell type

value: B cells

tag: tissue


title: Sample 34: I1_1_L2

tag: subset


title: Sporadic MPNST - resection [sMPNST12]

description:
sMPNST12
Primary tumor


title: Sporadic MPNST - resection [sMPNST8]

description:
sMPNST8
Primary tumor


title: Sample 31: I1_1_H1

value: Heavy


title: Plasma, healthy [Con-1 Vumc]

description: Con-1 Vumc

value: F


title: Sporadic MPNST - resection [sMPNST6]

description:
sMPNST6
Primary tumor


title: Sporadic MPNST - resection [sMPNST7]

description:
sMPNST7
Primary tumor


title: Sporadic MPNST - resection [sMPNST9]

description:
sMPNST9
Primary tumor


title: Plasma, healthy [Con-6 Vumc]

description: Con-6 Vumc


title: Plasma, healthy [Con-5 Vumc]

description: Con-5 Vumc


title: Sporadic MPNST - resection [sMPNST5]

description:
sMPNST5
Primary tumor


title: Sample 30: H5_L4

value: Peripheral blood

value: Plasmacyte

value: December 2, 2014


title: Sample 37: I1_1_H4

value: First Infection


title: Sample 33: I1_1_H2


title: Plasma, distal CCA [49CCA Vumc]

description: 49CCA Vumc

value: Distal cholangiocarcinoma


title: Sample 35: I1_1_H3

value: Memory


title: Sample 29: H5_H4


title: Sporadic MPNST - resection [sMPNST3]

description:
sMPNST3
Primary tumor


title: Sporadic MPNST - resection [sMPNST2]

description:
sMPNST2
Primary tumor


title: Sample 27: H5_H3


title: Sporadic MPNST - resection [sMPNST10]

description:
sMPNST10
Primary tumor


title: Plasma, distal CCA [45CCA Vumc]

description: 45CCA Vumc


title: Sample 26: H5_L2

value: Naïve

value: Light - Kappa and Lambda


title: Plasma, healthy [Con-3 Vumc]

description: Con-3 Vumc


title: Plasma, distal CCA [50CCA Vumc]

description: 50CCA Vumc


title: Sample 25: H5_H2


title: Plasma, distal CCA [42CCA Vumc]

description: 42CCA Vumc


title: Sample 28: H5_L3


title: Plasma, distal CCA [53CCA Vumc]

description: 53CCA Vumc


title: Sample 24: H5_L1

value: Immature


title: plexiform neurofibroma-resection [NF-20]

description:
NF-20
Pair with malignant peripheral nerve sheath tumor MPNST-19

data_processing: The expression (CT value) of a specific miRNA in a sample was normalized to the median CT of all detectable miRNAs in that sample. Subsequently the normalized relative expression (2-ΔCT) was calculated for each miRNA. The normalized miRNA expression data were log 2 transformed and median centered to acquire the relative expression values that were used for hierarchical clustering analyses using Cluster-3.0 and Java TreeView for visualization. The clustering was based on the uncentered correlation as a distance metric using average linkage. A paired Student T-test was used to determine statistical significance between distinct groups of expression data and the Benjamini-Hochberg false discovery rate (FDR) was used to control for multiple testing. For each miRNA, a detection limit of 55% was applied and those with detection lower than 55% were eliminated. In the matrices, blue cells designate flagged wells whereas green cells indicate wells with undetermined value which were arbitrarily set at the highest CT value measured in that particular sample.

treatment_protocol: Neurofibromatosis type 1 patients from which both plexiform neurofibroma as well as MPNST resection samples were available, were identified in the Erasmus Medical Center patient files. Formalin-fixed paraffin-embedded (FFPE) tissue blocks from resection material of the untreated, primary tumors comprising 9 plexiform neurofibroma/MPNST pairs, were collected from the Erasmus MC tissue bank. Hematoxylin-eosin-stained sections of these samples were examined by an expert pathologist to confirm the initial histopathological diagnosis.

value: Neurofibromatosis type 1

value: plexiform neurofibroma


title: NF1 derived MPNST-resection [MPNST-19]

description:
MPNST-19
Pair with plexiform neurofibroma sample NF-20

value: neurofibromatosis type 1 associated malignant peripheral nerve sheath tumor


title: NF1 derived MPNST-resection [MPNST-21]

description:
MPNST-21
Pair with plexiform neurofibroma sample NF-22


title: plexiform neurofibroma-resection [NF-17]

description:
NF-17
Pair with malignant peripheral nerve sheath tumor MPNST-16


title: plexiform neurofibroma-resection [NF-22]

description:
NF-22
Pair with malignant peripheral nerve sheath tumor MPNST-21


title: Sample 23: H5_H1


title: NF1 derived MPNST-resection [MPNST-16]

description:
MPNST-16
Pair with plexiform neurofibroma sample NF-17


title: Sample 22: H4_L4

value: November 25, 2014


title: Plasma, healthy [Con-15 Vumc]

description: Con-15 Vumc

value: Healthy


title: 48_hpi_S3

organism: Asparagus officinalis

tag: genotype

value: Susceptible

value: Stem

tag: infection

value: Phomopsis asparagi

value: 48 hpi


title: 48_hpi_S1


title: Plasma, healthy [Con-2 Vumc]

description: Con-2 Vumc

value: M


title: 48_hpi_S2


title: Sample 19: H4_H3

value: B cells

value: Peripheral blood

tag: chain type

value: Heavy


title: plexiform neurofibroma-resection [NF-18]

description:
NF-18
Pair with malignant peripheral nerve sheath tumor MPNST-15


title: NF1 derived MPNST-resection [MPNST-15]

description:
MPNST-15
Pair with plexiform neurofibroma sample NF-18


title: plexiform neurofibroma-resection [NF-9]

description:
NF-9
Pair with malignant peripheral nerve sheath tumor MPNST-13


title: Sample 20: H4_L3

value: Memory

tag: irepertoire barcode


title: Sample 18: H4_L2

value: Naïve


title: Plasma, distal CCA [38CCA Vumc]

description: 38CCA Vumc

tag: age

value: Distal cholangiocarcinoma


title: Plasma, distal CCA [47CCA Vumc]

description: 47CCA Vumc


title: NF1 derived MPNST-resection [MPNST-13]

description:
MPNST-13
Pair with plexiform neurofibroma sample NF-9


title: Sample 17: H4_H2


title: plexiform neurofibroma-resection [NF-10]

description:
NF-10
Pair with malignant peripheral nerve sheath tumor MPNST-12


title: Sample 16: H4_L1

value: Immature

value: Light - Kappa and Lambda


title: Control_S3

description: Control

value: Control


title: NF1 derived MPNST-resection [MPNST-12]

description:
MPNST-12
Pair with plexiform neurofibroma sample NF-10

value: Neurofibromatosis type 1

value: neurofibromatosis type 1 associated malignant peripheral nerve sheath tumor


title: Sample 15: H4_H1

value: Healthy

value: November 25, 2014


title: Control_S1

description: Control

value: Susceptible

value: Stem


title: 24_hpi_S1

value: Phomopsis asparagi

value: 24 hpi


title: plexiform neurofibroma-resection [NF-5]

description:
NF-5
Pair with malignant peripheral nerve sheath tumor MPNST-6

value: plexiform neurofibroma


title: Sample 13: H3_H4

value: B cells

value: Peripheral blood

value: Plasmacyte

value: November 18, 2014


title: Sample 14: H3_L4


title: NF1 derived MPNST-resection [MPNST-6]

description:
MPNST-6
Pair with plexiform neurofibroma sample NF-5


title: Sample 21: H4_H4

value: Heavy


title: Control_S2

description: Control


title: Sample 12: H3_L3

value: Memory


title: plexiform neurofibroma-resection [NF-11]

description:
NF-11
Pair with malignant peripheral nerve sheath tumor MPNST-4


title: 24_hpi_S3


title: NF1 derived MPNST-resection [MPNST-4]

description:
MPNST-4
Pair with plexiform neurofibroma sample NF-11


title: Sample 11: H3_H3


title: Sample 10: H3_L2

value: Naïve

value: Light - Kappa and Lambda


title: C3-L12-CUL-RNA

city: Salamanca

first: Adrian

last: Montano

address: Campus Miguel de Unamuno SN

country: Spain

institute: Cancer research center

data_processing:
Align to reference genome, STAR
Generate normalized genome browser track
Generate count matrix (samples & genes). featureCounts
Differential Expression Analysis.DESeq2
Genome_build: hg19

source_name: REH cell line (ACC 22)

growth_protocol: Cells were maintained in RPMI 1640 (Life Technologies, Carlsbad, California, USA) supplemented with 15% fetal bovine serum (FBS) and 1% of Penicillin/ Streptomycin (P/S) (Life Technologies)

extract_protocol:
Total RNA extraction was performed with the RNeasy Kit (Qiagen) as suggested by the manufacturer.
RNA-seq was performed by using TruSeq Stranded mRNA (Illumina). In all samples, RNA was analyzed following manufacturer’s recommendations for the protocol “TruSeq Stranded mRNA Reference Guide - Illumina”. Libraries were sequenced in the NextSeq550 platform (Illumina) according to manufacturer´s description with a read length of 2 × 75 nucleotides.

value: cell line established from the peripheral blood

tag: clon id

value: Control

value: Wild type


title: 24_hpi_S2


title: plexiform neurofibroma-resection [NF-7]

description:
NF-7
Pair with malignant peripheral nerve sheath tumor MPNST-2

value: Neurofibromatosis type 1


title: C21-L12-CUL-RNA

value: E/R KO


title: C9-L12-CUL-RNA


title: C14-L12-CUL-RNA


title: Sample 9: H3_H2

tag: health status

value: Healthy


title: C1-L12-CUL-RNA


title: Forebrain_RNA_R306C_rep10

city: Boston

first: Lisa

middle: D.

last: Boxer

state: MA

address: 220 Longwood Ave., Goldenson Bldg Rm 405

department: Neurobiology

institute: Harvard Medical School

hyb_protocol: 100ng RNA was hybridized to capture probes and reporter probes for 16 hours at 65°C.

scan_protocol: Hybridized RNA was scanned with the nCounter Sprint Profiler following the manufacturer's instructions.

data_processing: Nanostring data were analyzed with the nSolver software (v4.0) using the default mRNA parameters, including quality control, no background subtraction or thresholding, and normalization to positive controls and housekeeping genes.

label: Fluorescent barcodes

source_name: Forebrain tissue

label_protocol: standard NanoString protocol

extract_protocol: Forebrain (cortex and hippocampus) was dissected from 10 8-week-old male MeCP2 knock-out and 10 wild-type littermate controls and 10 8-to-12-week-old male R306C and 10 WT littermate controls and flash frozen. Tissue was removed from dry ice and placed directly into a dounce with 5 mL of Homogenization buffer (HB: 250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine KOH pH 7.8, 0.04% BSA, 5 µg/mL Actinomycin D, and RNAsin (Promega)). After 10 strokes with the tight pestle, a 5% Igepal (Sigma) solution in HB was added to a final concentration of 0.32%, followed by five additional strokes with the tight pestle. At this point, 200 μL of lysate was pipetted into a tube with 600 µL Trizol LS (Invitrogen) as the “whole cell” sample. Total RNA was chloroform extracted and purified with the Qiagen RNeasy Micro Kit with on-column DNase treatment.

tag: strain

value: 8-12 weeks

tag: gender

value: Male

value: MeCP2 R306C


title: NF1 derived MPNST-resection [MPNST-2]

description:
MPNST-2
Pair with plexiform neurofibroma sample NF-7

value: neurofibromatosis type 1 associated malignant peripheral nerve sheath tumor


title: Forebrain_RNA_R306C_rep9


title: Sample 8: H3_L1

value: B cells

value: Peripheral blood

value: Immature

tag: time point


title: REH-L12-CUL-RNA

value: REH cell


title: Forebrain_RNA_R306C_rep8


title: Sample 7: H3_H1

value: Heavy

value: November 18, 2014


title: M1981-3

city: Beijing

first: Hao

last: Dong

address: Huatuo road NO.31

institute: National Institutes for Food and Drug Control

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
mapsplice mapping to reference genome
count counting
Genome_build: brucella melitensis m28
Supplementary_files_format_and_content: TXT file contain counts for each sample

organism: Brucella melitensis

source_name: Gram-negative bacteria

growth_protocol: Brucella melitensis M1981 and RM57 strains were grown in TSB at 37℃ until the log phase was reached

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen).
RNA library using standard Ion proton RNA-Seq Kit v2.0 protocol

treatment_protocol: Brucella melitensis M1981 was obatined from IVDC, and the RM57 strains was induced from its smooth type parent strain M1981 using serum of rough type brucellosis strains


title: M1981-1


title: M1981-2


title: Sample 6: H2_L2

data_processing:
FASTQ files were submitted to iRepertoire for analysis using their iRmap program (Wang et al., 2010).
Briefly, sequence reads were de-multiplexed according to barcode sequences at the 5’ end of reads from the BCR heavy constant regions. Reads were then trimmed according to their base qualities with a 2-base sliding window.
Trimmed paired-end reads were joined together through overlapping alignment with a modified Needleman-Wunsch algorithm.
The merged reads were mapped using a Smith-Waterman algorithm to germline V, D, J, and C reference sequences downloaded from the IMGT web site (Lefranc, 2003).
To define the CDR3 region, the position of CDR3 boundaries of reference sequences from the IMGT database were migrated onto reads through mapping results, and the resulting CDR3 regions were extracted and translated into amino acids.
Genome_build: IMGT human BCR
Supplementary_files_format_and_content: Comma-separated values files were generated by iRepertoire for each sample.  Each files contains the nucleic acid and predicted amino acid sequence of the CDR3 regions, isotypes, assigned V, D, and J genes, and read counts.

source_name: B cells

value: Naïve

value: Light - Kappa and Lambda

value: November 3, 2014


title: Forebrain_RNA_R306C_rep6


title: Forebrain_RNA_R306C_rep5


title: Forebrain_RNA_R306C_rep7


title: RM57-3


title: Forebrain_RNA_R306C_rep4


title: Sample 3: H2_H1


title: RM57-2


title: Forebrain_RNA_R306C_rep3


title: 14040_3v_LRL Kp11_vaccinated_Day3

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

data_processing:
bcl2fastq.pl basecall converter v2.2
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Macaque whole genome using hisat2
normalization and comparisons were run using deseq2 on the original file host_matrix30.txt
Genome_build: GCF_000364345.1_Macaca_fascicularis_5.0_genomic.fna
Supplementary_files_format_and_content: filtered, aligned, raw counts from all samples in one matrix;

organism: Macaca fascicularis

source_name: Lung Right Lobe

growth_protocol: CPS2 was extracted from bacterial culture supernatant, residual endotoxin was inactivated by incubation of purified CPS2 with 0.1 N NaOH in 95% ethanol for 1 h at 37C. The pH of the solution was neutralized with 2 N acetic acid and CPS2 was collected by centrifugation at 2000g for 10 min. The pellet was air dried and resuspended in sterile water

extract_protocol:
RNA was purified initially by using a PureLink  RNA Mini Kit (Life Technologies, Carlsbad, CA). DNA was removed from purified RNA samples by treatment with TURBO DNase (Life Technologies, Grand Island, NY) for 45 min at 37 C, and RNA was purified again using an RNeasy Mini Kit (Qiagen
Truseq RNA-seq with Poly dT pullout

treatment_protocol: Five sham-vaccinated animals received 0.6 ml of injection grade saline combined with adjuvant instead of purified CPS2;Five animals were inoculated with up to 500 μg of purified K. pneumoniae CPS2 in 0.6 ml injection grade saline mixed 1:1 with TiterMax Gold adjuvant (Sigma-Aldrich).

tag: animal id

tag: vaccination

value: ST258 CPS2

value: Lung Right Lobe

tag: treatment

value: vaccinated

tag: time


title: Sample 1: H1_H1

first: Erin

last: Mitsunaga

address: 300 Pasteur Drive

extract_protocol:
Total RNA was extracted from flow cytometry-sorted human peripheral blood B cells with the Qiagen AllPrep RNA/DNA Micro Kit (Cat. # 80284) per the manufacturer's instructions.
Targeted RNA sequencing libraries were made using human B cell-specific primers from iRepertoire (Huntsville, AL) according to the company's instructions.  Briefly, two rounds of RT-PCR were performed for each chain type (heavy or light chain) and the resulting B cell receptor amplicons were sequenced.

tag: cell type

value: Healthy

value: September 27, 2014


title: RM57-1


title: Experimental cDNA replicate 2 for MPRA2

description:
MPRA2_cDNA_rep2
Experimental cDNA library barcode tag sequencing
MPRAcounts.tsv.gz

value: H9-derived Neural Stem Cells

tag: passage


title: Experimental cDNA replicate 1 for MPRA2

description:
MPRA2_cDNA_rep1
Experimental cDNA library barcode tag sequencing
MPRAcounts.tsv.gz


title: 14039_3v_LRL Kp11_vaccinated_Day3

tag: tissue


title: Forebrain_RNA_R306C_rep2

value: 8-12 weeks

value: Male

tag: genotype

value: MeCP2 R306C


title: Experimental plasmid DNA replicate 2 for MPRA2

description:
MPRA2_pDNA_rep2
Experimental plasmid DNA library barcode tag sequencing
MPRAcounts.tsv.gz


title: 14038_3v_LRL Kp11_vaccinated_Day3


title: Sample 5: H2_H2

value: B cells

value: Peripheral blood

tag: subset


title: Forebrain_RNA_WT_rep10

value: WT


title: Forebrain_RNA_WT_rep9


title: Forebrain_RNA_R306C_rep1


title: 14037_7s_LRL Kp16_sham_Day7

value: injection grade saline with TiterMax Gold adjuvant

value: sham


title: Sample 4: H2_L1

value: Immature

tag: chain type


title: Experimental plasmid DNA replicate 1 for MPRA2

description:
MPRA2_pDNA_rep1
Experimental plasmid DNA library barcode tag sequencing
MPRAcounts.tsv.gz


title: 14036_7s_LRL Kp16_sham_Day7


title: Inert library for MPRA2

description:
MPRA2_inert
Inert library long reads are used to establish barcode-enhancer fragment connections
MPRAcounts.tsv.gz


title: Forebrain_RNA_WT_rep8


title: Inert library for MPRA1

description:
MPRA1_inert
Inert library long reads are used to establish barcode-enhancer fragment connections
COUNTS_ANNOTATED.txt.gz


title: 14035_7s_LRL Kp16_sham_Day7


title: Forebrain_RNA_WT_rep7


title: Forebrain_RNA_WT_rep6


title: 14034_7s_LRL Kp15_sham_Day7


title: Sample 2: H1_L1

value: Light - Kappa and Lambda

tag: irepertoire barcode


title: Forebrain_RNA_WT_rep5

tag: age


title: 14033_7s_LRL Kp15_sham_Day7


title: Forebrain_RNA_WT_rep4


title: 14031_7v_LRL Kp9 _vaccinated_Day7


title: 14030_7v_LRL Kp9 _vaccinated_Day7


title: Forebrain_RNA_WT_rep3


title: Forebrain_RNA_WT_rep2


title: 14028_7v_LRL Kp8 _vaccinated_Day7


title: Forebrain_RNA_MeCP2_KO_rep10

value: 8 weeks

value: MeCP2 KO


title: 14029_7v_LRL Kp9 _vaccinated_Day7

value: ST258 CPS2

value: Lung Right Lobe


title: 14027_7v_LRL Kp8 _vaccinated_Day7

value: vaccinated


title: Forebrain_RNA_MeCP2_KO_rep8


title: 14026_7v_LRL Kp8 _vaccinated_Day7


title: 14025_5s_LLL Kp12_sham_Day5

source_name: Lung Left Lobe

value: Lung Left Lobe


title: Forebrain_RNA_MeCP2_KO_rep7


title: 14032_7s_LRL Kp15_sham_Day7


title: Forebrain_RNA_MeCP2_KO_rep9


title: 14024_5s_LLL Kp12_sham_Day5


title: Forebrain_RNA_MeCP2_KO_rep5


title: 14023_5s_LLL Kp12_sham_Day5


title: Forebrain_RNA_WT_rep1


title: Forebrain_RNA_MeCP2_KO_rep4


title: 14022_5v_LRL Kp10_vaccinated_Day5


title: Forebrain_RNA_MeCP2_KO_rep6


title: Forebrain_RNA_MeCP2_KO_rep3


title: Forebrain_RNA_MeCP2_KO_rep2


title: 14021_5v_LRL Kp10_vaccinated_Day5


title: 14019_3s_LRL Kp14_sham_Day3


title: 14018_3s_LRL Kp14_sham_Day3


title: Forebrain_RNA_MeCP2_WT_rep10


title: Forebrain_RNA_MeCP2_KO_rep1


title: 14017_3s_LRL Kp14_sham_Day3


title: Forebrain_RNA_MeCP2_WT_rep9


title: Forebrain_RNA_MeCP2_WT_rep8


title: N2: paracancerous tissue of PCa

city: Shanghai

first: jin

last: wang

address: 2901 Caolang Road, Jinshan District,

institute: Shanghai Public Health Clinical Center, Fudan University,

description: Gene expression for paracancerous tissue of PCa

hyb_protocol: The microarray  hybridization was performed following the manufacturer’s standard protocols using a  Gene Expression Hybridization Kit (Santa Clara, CA, US) in a Hybridization Oven  (Santa Clara, CA, US).

scan_protocol: The hybridized slides were washed, fixed and finally scanned  to obtain images by an Agilent Microarray Scanner (Santa Clara, CA, US).

data_processing: The data  were extracted with Feature Extraction software 10.7 (CA, US), and the raw data were  normalized by the Quantile algorithm in the limma package in R.

source_name: paracancerous tissue of PCa

label_protocol: The total RNA was amplified and labeled by a Low Input Quick Amp WT Labeling Kit (Santa Clara,  CA, US), and the labeled cRNAs were purified by an RNeasy mini kit.

extract_protocol: The total RNA was extracted and purified using TRIzol reagent (Invitrogen) and an RNeasy Mini Kit (Qiagen, USA) following the manufacturer’s instructions. The total  RNA was quantified by a NanoDrop-2000 spectrophotometer (NanoDrop, USA). The selected RNA samples were assessed by an Agilent Bioanalyzer 2100 (CA, US) to  inspect the RNA integrity.

value: paracancerous tissue

value: male


title: N3: paracancerous tissue of PCa


title: 14016_3s_LLL Kp13_sham_Day3


title: T3: tumor tissue of PCa

description: Gene expression for tumor tissue of PCa

source_name: tumor tissue of PCa

value: tumor tissue of PCa


title: T1: tumor tissue of PCa

description: Gene expression for tumor tissue of PCa


title: Forebrain_RNA_MeCP2_WT_rep7

value: Male


title: 14020_5v_LRL Kp10_vaccinated_Day5


title: N4: paracancerous tissue of PCa


title: T4: tumor tissue of PCa

description: Gene expression for tumor tissue of PCa


title: 14015_3s_LLL Kp13_sham_Day3


title: 14014_3s_LLL Kp13_sham_Day3


title: Forebrain_RNA_MeCP2_WT_rep6


title: T2: tumor tissue of PCa

description: Gene expression for tumor tissue of PCa


title: N1: paracancerous tissue of PCa


title: Forebrain_RNA_MeCP2_WT_rep5


title: Forebrain_RNA_MeCP2_WT_rep4


title: 14013_3v_LRL Kp7 _vaccinated_Day3


title: 14011_3v_LRL Kp7 _vaccinated_Day3


title: Forebrain_RNA_MeCP2_WT_rep2


title: 14012_3v_LRL Kp7 _vaccinated_Day3


title: Forebrain_RNA_MeCP2_WT_rep3


title: fliF II

status: Public on Nov 25 2019

city: Braunschweig

first: Matthias

last: Preusse

address: Inhoffenstr. 7

country: Germany

institute: Helmholtz Centre for Infection Research

description:
S. Typhimurium planktonic culture
F2

data_processing:
RNA-seq reads were mapped to the Salmonella Typhimurium UK-1 (NC_016863.1) genome using bowtie2 with the option "no-1mm-upfront"
Differential expression was estimated using the R library edgeR and the function glmTreat
Genome_build: gi|378987404|ref|NC_016863.1|
Supplementary_files_format_and_content: The processed file "rpg_table.csv" contains reads per gene. The file "edgeR_result.csv" contains log2FC and adjusted p values (false discovery rate, FDR) for each combination between the three samples.

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: S. Typhimurium UK-1 derivate

growth_protocol: LB medium at 37°C and 140 rpm until OD600=2.0.

extract_protocol:
Using Rneasy kit (Qiagen) plus Qiashredder columns.
Customized protocol (Dötsch et al., PloS ONE, 2012). Briefly, eukariotic RNA was depleted using MICROBEnrich Kit (both for tumor samples and control sampels), subsequently bacterial rRNA was depleted using MICROBExpress kit with the Pseudomonas module (Ambion) and fragmented by sonication using Covaris Adaptive Acoustics device (Covaris). Upon ligation of barcoded adapters, reverse transcription with SuperScript II kit (Invitrogen) followed. Amplification was done by PCR using Illumina platform compatible primers. Established cDNA library was normalized by double strand specific nuclease treatment (Evrogen) according DSN Normalization Sample Preparation Guide from Illumina.

treatment_protocol: Cells from 2 pooled cultures were harvested by addition of the same volume of RNA-protect buffer (Qiagen) and centrifugation. The RNA was stored at -70°C.

tag: strain/genotype

value: SF102 + {delta}fliF (EM6333)


title: WDH_Normal

city: Guangzhou

first: hu

middle: xue

last: ting

address: NO.107 Yanjiangxi Road  Guangzhou

institute: Huxueting

description: Gene expression data

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays (6x7K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Axon GenePix 4000B Scanner.

data_processing: Quantile normalization and subsequent data processing were performed using the R software package. Differentially expressed circRNAs with statistical significance between two groups were identified through Volcano Plot filtering. Differentially expressed circRNAs between two samples were identified through Fold Change filtering. Hierarchical Clustering was performed to show the distinguishable circRNAs expression pattern among samples.

source_name: WDH_adjacent non-cancerous tissues

label_protocol: total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing random primer according to Arraystar’s Super RNA Labeling protocol (Arraystar Inc.)

extract_protocol: Total RNA from each sample was quantified using the NanoDrop ND-1000. The sample preparation and microarray hybridization were performed based on the Arraystar’s standard protocols

treatment_protocol: Surgical resection of esophageal cancer tissue and corresponding adjacent tissues, immediately placed in liquid nitrogen preservation

value: Normal esophageal epithelial tissue


title: fliHIJ II

description:
S. Typhimurium planktonic culture
HIJ2

value: SF102 + {delta}fliHIJ (EM6331)


title: WDH_Cancer

description: Gene expression data

source_name: WDH_ESCC tisues

value: esophageal squamous cancer tissue


title: ZYB_Cancer

description: Gene expression data

source_name: ZYB_ESCC tisues


title: LXZ_Cancer

description: Gene expression data

source_name: LXZ_ESCC tisues


title: fliF I

description:
S. Typhimurium planktonic culture
F1


title: Forebrain_RNA_MeCP2_WT_rep1

value: WT


title: LXZ_Normal

description: Gene expression data

source_name: LXZ_adjacent non-cancerous tissues


title: fliHIJ I

description:
S. Typhimurium planktonic culture
HIJ1


title: SF102 II

description:
S. Typhimurium planktonic culture
A2


title: SF102 I

description:
S. Typhimurium planktonic culture
A1


title: OM431.RNA-seq.rep2

first: Bao-Fa

last: Sun

address: Da-Tun Road

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

data_processing:
For RNA-seq and MeRIP-seq, reads were processed using Cutadapt software (version 1.18) and Trimmomatic (version 0.36). The remained reads were aligned to human genome (version hg19) using Hisat2 (version 2.1.0).
For MeRIP-seq data, MACS2 software (version 2.0.10) was used for m6A peak calling, and m6A peaks were annotated by perfroming BEDTools’ intersectBed (version 2.27.1).
For miCLIP-seq, pre-processing was performed by using CLIP Tool Kit (CTK). The remined reads were aligned to human genome (version hg19) using BWA software (version 0.7.10).
m6A locus were detected by performing Program CIMS.pl for miCLIP-seq data.
miCLIP-seq m6A locus were annotated by using BEDTools’ intersectBed (version 2.27.1).
Genome_build: hg19
Supplementary_files_format_and_content: miCLIP-seq_m6A_single-nucleotide-resolution_locus.xlsx.gz: miCLIP-seq_m6A_single-nucleotide-resolution_locus
Supplementary_files_format_and_content: MeRIP-seq_m6A_peak_locus.xlsx.gz: MeRIP-seq_m6A_peak_locus
Supplementary_files_format_and_content: Reads_count_featureCounts.xlsx.gz: Reads count for all samples

source_name: Ocular melanoma cell line

extract_protocol:
For RNA-seq, total RNA was extracted from samples using an EZ-press RNA Purification Kit (B0004).
For miCLIP-seq, mRNA was isolated from tumor and normal cell lines by using Dynabeads mRNA Purification Kit (Life Technologies, 61006).
For RNA-seq, libraries were constructed from  100 ng of total RNA using an Illumina TruSeq RNA Sample Prep Kit (San Diego, CA, USA) following the manufacturer’s protocol.
For MeRIP-seq, purified mRNA was randomly fragmented to approximately 100 nucleotides using Ambion RNA fragmentation reagents and then subjected to IP with an anti-m6A antibody (202003, Synaptic Systems) and protein A magnetic beads (88845, Pierce) in meRIP buffer (150 mM NaCl, 10 mM Tris-HCl, pH 7.4, 0.1% NP-40) supplemented with RNase inhibitor. m6A-containing mRNA fragments were eluted with m6A in MeRIP buffer and purified using TRIzol reagent.
For miCLIP-seq, mRNA was fragmented to ~100 nucleotides using fragmentation reagent (Life Technologies, AM8740), and incubated with 5 µg of an anti-m6A antibody (Abcam, ab151230) in 450 µL of IP buffer (50 mM Tris, 100 mM NaCl, 0.05% NP-40, adjusted to pH 7.4) under gentle rotation at 4°C for 2 h. The mixture was transferred to a clear flat-bottom 96-well plate (Corning) on ice and irradiated three times with 0.15 J/cm2 at 254 nm using a CL-1000 Ultraviolet Crosslinker (UVP). After irradiation, the mixture was collected and incubated with 50 µL of prewashed Dynabeads Protein A (Life Technologies, 1001D) at 4°C for 2 h. After extensive washing twice with high-salt buffer (50 mM Tris, 1 M NaCl, 1 mM EDTA, 1% NP-40, 0.1% SDS, adjusted to pH 7.4) and twice with IP buffer, the samples on the beads were subjected to dephosphorylation with T4 PNK (NEB, M0201L) at 37°C for 20 min. The RNA was then eluted from the beads by proteinase K (Sigma, P2308) treatment at 55°C for 1 h, followed by phenol-chloroform extraction and ethanol precipitation. The purified RNA was subjected to library construction using SMARTer smRNA-Seq Kit for Illumina (Clontech Laboratories, 635030) according to the manufacturer’s instructions.

value: Ocular melanoma cell


title: OCM1a.RNA-seq.rep1


title: OM431.RNA-seq.rep1


title: PIG1.RNA-seq.rep2

source_name: Melanocyte cell line

value: Melanocyte cell


title: PIG1.RNA-seq.rep1


title: OCM1a.RNA-seq.rep2


title: CRMM1.RNA-seq.rep2


title: OCM1.RNA-seq.rep1


title: OCM1.RNA-seq.rep2


title: CRMM1.RNA-seq.rep1


title: CM2005.1.RNA-seq.rep2


title: CM2005.1.RNA-seq.rep1


title: CON_CD8_5

type: genomic

city: Pittsburgh

first: Amr

last: Sawalha

address: 4401 Penn Avenue

institute: University of Pittsburgh

description: healthy CD8+ T cell

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: Methylation beta values were calculated from raw intensity values using GenomeStudio Methylation module software (Illumina; ver 1.9.0) after subtracting background, normalization to control probes, error correction using the Illumina custom model, and correction for false discovery rate.

source_name: CD8+ T cell DNA

label_protocol: standard Illumina protocol

extract_protocol: Peripheral blood mononuclear cells (PBMCs) were extracted from whole blood via Ficoll-Paque PLUS density centrifugation (GE Healthcare Bio-Sciences). Total T cells were isolated using negative selection by magnetic bead separation with the Human Pan T cell Isolation II kit (Miltenyi Biotec). Flow cytometry sorting was used to isolate CD3+CD56-TCRab+CD8+ T cells using the following fluorophore-conjugated antibodies: APC anti-human CD56 (clone: HCD56), FITC anti-human CD8a (clone: RPA-T8), Pacific Blue anti-human CD3 (clone: HIT3a), and PE anti-human alpha/beta-TCR (clone: IP26) (BioLegend). DNA was extracted from CD8+ T cells using the DNeasy Blood and Tissue kit (Qiagen) and bisulfite converted with the EZ DNA Methylation kit (Zymo Research) for DNA methylation analysis.

value: CD8+ T cell

tag: disease status

value: healthy


title: PIG1.miCLIP-seq.rep1

description: miCLIP-seq_m6A_single-nucleotide-resolution_locus.xlsx.gz

molecule: polyA RNA


title: OM431.miCLIP-seq.rep1


title: OCM1a.miCLIP-seq.rep2


title: OCM1a.miCLIP-seq.rep1


title: PIG1.miCLIP-seq.rep2


title: OM431.miCLIP-seq.rep2


title: OCM1.miCLIP-seq.rep1


title: CRMM1.miCLIP-seq.rep2


title: CM2005.1.miCLIP-seq.rep1


title: CM2005.1.miCLIP-seq.rep2


title: OCM1.miCLIP-seq.rep2